data_X5J # _chem_comp.id X5J _chem_comp.name "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)amino]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H26 N8 O9 P2 S2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-11-30 _chem_comp.pdbx_modified_date 2021-05-28 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 648.546 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X5J _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7KVX _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal X5J C4 C1 C 0 1 Y N N 41.104 7.974 19.433 5.009 -2.185 -0.199 C4 X5J 1 X5J C5 C2 C 0 1 Y N N 39.626 9.322 18.684 6.755 -0.919 -0.413 C5 X5J 2 X5J C6 C3 C 0 1 Y N N 45.906 9.223 16.679 -7.354 1.111 -0.236 C6 X5J 3 X5J C7 C4 C 0 1 Y N N 39.115 8.061 18.490 5.754 -0.147 0.189 C7 X5J 4 X5J C8 C5 C 0 1 N N N 38.823 10.453 18.269 8.011 -0.320 -0.668 C8 X5J 5 X5J C10 C6 C 0 1 N N N 45.816 5.660 15.777 -3.994 1.769 1.209 C10 X5J 6 X5J C13 C7 C 0 1 N N N 42.136 4.016 20.770 0.850 -3.131 0.529 C13 X5J 7 X5J C15 C8 C 0 1 N N R 46.288 6.879 16.539 -5.159 0.837 0.859 C15 X5J 8 X5J C17 C9 C 0 1 N N R 40.786 3.905 20.113 1.322 -1.739 0.950 C17 X5J 9 X5J C20 C10 C 0 1 N N R 39.929 5.743 18.960 3.368 -0.603 0.885 C20 X5J 10 X5J C1 C11 C 0 1 Y N N 45.155 10.354 16.459 -7.889 0.141 0.614 C1 X5J 11 X5J C2 C12 C 0 1 Y N N 45.673 11.561 16.870 -9.224 -0.184 0.480 C2 X5J 12 X5J C3 C13 C 0 1 Y N N 47.508 10.520 17.635 -9.416 1.344 -1.230 C3 X5J 13 X5J C9 C14 C 0 1 N N N 37.194 8.683 17.556 7.176 1.671 0.271 C9 X5J 14 X5J C11 C15 C 0 1 N N N 46.153 6.445 17.973 -4.580 -0.461 0.286 C11 X5J 15 X5J C12 C16 C 0 1 N N N 43.576 4.534 16.162 -1.756 1.855 0.080 C12 X5J 16 X5J C14 C17 C 0 1 N N R 44.922 4.876 16.725 -2.694 1.003 0.937 C14 X5J 17 X5J C16 C18 C 0 1 N N S 44.846 5.707 17.968 -3.060 -0.284 0.191 C16 X5J 18 X5J C18 C19 C 0 1 N N R 40.865 4.975 18.059 2.499 0.072 -0.185 C18 X5J 19 X5J C19 C20 C 0 1 N N R 40.889 3.574 18.657 1.210 -0.772 -0.243 C19 X5J 20 X5J N21 N1 N 0 1 Y N N 46.861 11.681 17.466 -9.950 0.432 -0.443 N21 X5J 21 X5J N22 N2 N 0 1 Y N N 47.101 9.294 17.273 -8.147 1.684 -1.137 N22 X5J 22 X5J N23 N3 N 0 1 Y N N 40.861 9.259 19.274 6.237 -2.154 -0.626 N23 X5J 23 X5J N24 N4 N 0 1 N N N 37.935 7.700 17.943 6.004 1.127 0.510 N24 X5J 24 X5J N25 N5 N 0 1 Y N N 40.068 7.199 18.967 4.665 -0.967 0.310 N25 X5J 25 X5J N26 N6 N 0 1 N N N 37.608 10.003 17.710 8.189 0.972 -0.315 N26 X5J 26 X5J N27 N7 N 0 1 N N N 35.990 8.442 16.983 7.385 2.982 0.618 N27 X5J 27 X5J N28 N8 N 0 1 N N N 45.380 7.991 16.255 -6.021 1.476 -0.138 N28 X5J 28 X5J O29 O1 O 0 1 N N N 39.200 11.623 18.415 8.911 -0.954 -1.192 O29 X5J 29 X5J O30 O2 O 0 1 N N N 40.892 7.151 15.207 0.658 1.922 -1.740 O30 X5J 30 X5J O31 O3 O 0 1 N N N 44.818 6.797 20.973 -1.097 -1.990 -1.283 O31 X5J 31 X5J O32 O4 O 0 1 N N N 42.855 5.743 16.028 -0.411 1.677 0.531 O32 X5J 32 X5J O33 O5 O 0 1 N N N 42.727 5.291 20.635 -0.543 -3.262 0.826 O33 X5J 33 X5J O34 O6 O 0 1 N N N 40.067 5.139 20.230 2.696 -1.780 1.341 O34 X5J 34 X5J O35 O7 O 0 1 N N N 44.788 4.896 19.126 -2.401 -1.398 0.795 O35 X5J 35 X5J O36 O8 O 0 1 N N N 40.426 5.047 16.716 2.189 1.413 0.199 O36 X5J 36 X5J O37 O9 O 0 1 N N N 39.798 2.709 18.264 0.060 0.064 -0.100 O37 X5J 37 X5J P38 P1 P 0 1 N N R 41.309 5.743 15.523 0.869 2.188 -0.299 P38 X5J 38 X5J P39 P2 P 0 1 N N R 44.352 5.408 20.621 -1.696 -2.567 -0.058 P39 X5J 39 X5J S40 S1 S 0 1 N N N 41.082 4.440 13.906 1.121 4.271 0.003 S40 X5J 40 X5J S41 S2 S 0 1 N N N 45.165 3.940 21.864 -3.143 -4.019 -0.598 S41 X5J 41 X5J H1 H1 H 0 1 N N N 42.006 7.578 19.875 4.358 -3.045 -0.245 H1 X5J 42 X5J H2 H2 H 0 1 N N N 45.249 5.966 14.885 -4.035 2.662 0.585 H2 X5J 43 X5J H3 H3 H 0 1 N N N 46.676 5.046 15.472 -4.046 2.048 2.261 H3 X5J 44 X5J H4 H4 H 0 1 N N N 42.020 3.798 21.842 1.009 -3.262 -0.541 H4 X5J 45 X5J H5 H5 H 0 1 N N N 42.806 3.272 20.315 1.411 -3.889 1.076 H5 X5J 46 X5J H6 H6 H 0 1 N N N 47.331 7.125 16.291 -5.736 0.617 1.757 H6 X5J 47 X5J H7 H7 H 0 1 N N N 40.221 3.105 20.614 0.711 -1.377 1.776 H7 X5J 48 X5J H8 H8 H 0 1 N N N 38.912 5.524 18.603 3.515 0.082 1.720 H8 X5J 49 X5J H9 H9 H 0 1 N N N 44.189 10.297 15.979 -7.273 -0.345 1.356 H9 X5J 50 X5J H10 H10 H 0 1 N N N 45.090 12.454 16.702 -9.672 -0.930 1.120 H10 X5J 51 X5J H11 H11 H 0 1 N N N 48.471 10.578 18.120 -10.036 1.826 -1.971 H11 X5J 52 X5J H12 H12 H 0 1 N N N 46.981 5.784 18.268 -4.815 -1.294 0.948 H12 X5J 53 X5J H13 H13 H 0 1 N N N 46.117 7.312 18.649 -4.996 -0.646 -0.704 H13 X5J 54 X5J H14 H14 H 0 1 N N N 43.045 3.853 16.844 -1.834 1.545 -0.962 H14 X5J 55 X5J H15 H15 H 0 1 N N N 43.690 4.053 15.179 -2.035 2.905 0.170 H15 X5J 56 X5J H16 H16 H 0 1 N N N 45.437 3.936 16.973 -2.210 0.758 1.881 H16 X5J 57 X5J H17 H17 H 0 1 N N N 44.002 6.411 17.915 -2.768 -0.199 -0.855 H17 X5J 58 X5J H18 H18 H 0 1 N N N 41.872 5.408 18.148 3.004 0.056 -1.149 H18 X5J 59 X5J H19 H19 H 0 1 N N N 41.858 3.099 18.447 1.161 -1.328 -1.179 H19 X5J 60 X5J H20 H20 H 0 1 N N N 36.976 10.709 17.390 9.042 1.404 -0.477 H20 X5J 61 X5J H21 H21 H 0 1 N N N 35.674 7.501 16.859 8.245 3.398 0.446 H21 X5J 62 X5J H22 H22 H 0 1 N N N 35.417 9.205 16.684 6.674 3.493 1.036 H22 X5J 63 X5J H23 H23 H 0 1 N N N 45.218 8.032 15.269 -5.659 2.154 -0.730 H23 X5J 64 X5J H24 H24 H 0 1 N N N 39.897 1.863 18.684 -0.780 -0.414 -0.128 H24 X5J 65 X5J H25 H25 H 0 1 N N N 41.495 3.314 14.407 -0.035 4.785 -0.454 H25 X5J 66 X5J H26 H26 H 0 1 N N N 44.812 4.358 23.043 -2.424 -4.918 -1.293 H26 X5J 67 # # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal X5J S40 P38 SING N N 1 X5J O30 P38 DOUB N N 2 X5J P38 O32 SING N N 3 X5J P38 O36 SING N N 4 X5J C10 C15 SING N N 5 X5J C10 C14 SING N N 6 X5J O32 C12 SING N N 7 X5J C12 C14 SING N N 8 X5J N28 C15 SING N N 9 X5J N28 C6 SING N N 10 X5J C1 C6 SING Y N 11 X5J C1 C2 DOUB Y N 12 X5J C15 C11 SING N N 13 X5J C6 N22 DOUB Y N 14 X5J O36 C18 SING N N 15 X5J C14 C16 SING N N 16 X5J C2 N21 SING Y N 17 X5J N27 C9 SING N N 18 X5J N22 C3 SING Y N 19 X5J N21 C3 DOUB Y N 20 X5J C9 N26 SING N N 21 X5J C9 N24 DOUB N N 22 X5J N26 C8 SING N N 23 X5J N24 C7 SING N N 24 X5J C16 C11 SING N N 25 X5J C16 O35 SING N N 26 X5J C18 C19 SING N N 27 X5J C18 C20 SING N N 28 X5J O37 C19 SING N N 29 X5J C8 O29 DOUB N N 30 X5J C8 C5 SING N N 31 X5J C7 C5 DOUB Y N 32 X5J C7 N25 SING Y N 33 X5J C19 C17 SING N N 34 X5J C5 N23 SING Y N 35 X5J C20 N25 SING N N 36 X5J C20 O34 SING N N 37 X5J N25 C4 SING Y N 38 X5J O35 P39 SING N N 39 X5J N23 C4 DOUB Y N 40 X5J C17 O34 SING N N 41 X5J C17 C13 SING N N 42 X5J P39 O33 SING N N 43 X5J P39 O31 DOUB N N 44 X5J P39 S41 SING N N 45 X5J O33 C13 SING N N 46 X5J C4 H1 SING N N 47 X5J C10 H2 SING N N 48 X5J C10 H3 SING N N 49 X5J C13 H4 SING N N 50 X5J C13 H5 SING N N 51 X5J C15 H6 SING N N 52 X5J C17 H7 SING N N 53 X5J C20 H8 SING N N 54 X5J C1 H9 SING N N 55 X5J C2 H10 SING N N 56 X5J C3 H11 SING N N 57 X5J C11 H12 SING N N 58 X5J C11 H13 SING N N 59 X5J C12 H14 SING N N 60 X5J C12 H15 SING N N 61 X5J C14 H16 SING N N 62 X5J C16 H17 SING N N 63 X5J C18 H18 SING N N 64 X5J C19 H19 SING N N 65 X5J N26 H20 SING N N 66 X5J N27 H21 SING N N 67 X5J N27 H22 SING N N 68 X5J N28 H23 SING N N 69 X5J O37 H24 SING N N 70 X5J S40 H25 SING N N 71 X5J S41 H26 SING N N 72 # # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor X5J SMILES ACDLabs 12.01 "c1nc6c(n1C2OC3COP(=O)(OC4CC(CC4COP(=O)(OC2C3O)S)Nc5ncncc5)S)N=C(NC6=O)N" X5J InChI InChI 1.03 "InChI=1S/C20H26N8O9P2S2/c21-20-26-17-14(18(30)27-20)24-8-28(17)19-16-15(29)12(35-19)6-34-38(31,40)36-11-4-10(25-13-1-2-22-7-23-13)3-9(11)5-33-39(32,41)37-16/h1-2,7-12,15-16,19,29H,3-6H2,(H,31,40)(H,32,41)(H,22,23,25)(H3,21,26,27,30)/t9-,10-,11+,12-,15-,16-,19-,38-,39-/m1/s1" X5J InChIKey InChI 1.03 DXJHOSYLPZBMEZ-FEFYGENMSA-N X5J SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](S)(=O)O[C@H]5C[C@@H](C[C@@H]5CO[P@](S)(=O)O[C@@H]3[C@@H]4O)Nc6ccncn6" X5J SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](S)(=O)O[CH]5C[CH](C[CH]5CO[P](S)(=O)O[CH]3[CH]4O)Nc6ccncn6" X5J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cncnc1N[C@@H]2C[C@@H]3CO[P@](=O)(O[C@@H]4[C@@H]([C@@H](CO[P@](=O)(O[C@H]3C2)S)O[C@H]4n5cnc6c5N=C(NC6=O)N)O)S" X5J SMILES "OpenEye OEToolkits" 2.0.7 "c1cncnc1NC2CC3COP(=O)(OC4C(C(COP(=O)(OC3C2)S)OC4n5cnc6c5N=C(NC6=O)N)O)S" # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier X5J "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,5R,7R,8R,10R,12aR,14R,15aS,16R)-7-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-16-hydroxy-14-[(pyrimidin-4-yl)amino]-2,10-disulfanyldecahydro-2H,10H-5,8-methano-2lambda~5~,10lambda~5~-cyclopenta[l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecine-2,10-dione" X5J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-9-[(1~{R},3~{R},6~{R},8~{R},10~{S},12~{R},15~{R},17~{R},18~{R})-18-oxidanyl-3,12-bis(oxidanylidene)-8-(pyrimidin-4-ylamino)-3,12-bis(sulfanyl)-2,4,11,13,16-pentaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.2.1.0^{6,10}]octadecan-17-yl]-1~{H}-purin-6-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site X5J "Create component" 2020-11-30 RCSB X5J "Initial release" 2021-06-02 RCSB ##